Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC3

Cell type

Cell type Class
Lung
Cell type
IMR-90
Primary Tissue
Lung
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
IMR90
cell line
IMR90
4oht
n/a
treatment
TNFa
chip antibody
SMC3 (ab9263)
passage
22-28

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixed cells were lysed and sonicated to generate 200-400 bp chromatin fragments before immunoprecipitation. Libraries were prepared using the NEBnext ultra II DNA-library prep kit for Illumina (E7645) according to manufacturers instructions except that size selection was performed during the final bead purification step using SPRIselect beads (B23319, Beckman Coulter)

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
44290840
Reads aligned (%)
98.5
Duplicates removed (%)
10.9
Number of peaks
1872 (qval < 1E-05)

hg19

Number of total reads
44290840
Reads aligned (%)
97.6
Duplicates removed (%)
11.2
Number of peaks
1571 (qval < 1E-05)

Base call quality data from DBCLS SRA